From a8fa445555ecdf1b2203ffd2dc4334249f3784ee Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Thu, 20 Sep 2007 14:53:50 +0000
Subject: [PATCH] test changes for addition of external_db_id and hcoverage to
XXXalignfeatures.
---
modules/t/dnaAlignFeatureAdaptor.t | 10 ++++++++--
modules/t/proteinAlignFeatureAdaptor.t | 10 ++++++++--
.../homo_sapiens/core/dna_align_feature.sql | 7 +++++--
modules/t/test-genome-DBs/homo_sapiens/core/meta.txt | 2 +-
.../homo_sapiens/core/protein_align_feature.sql | 9 ++++++---
5 files changed, 28 insertions(+), 10 deletions(-)
diff --git a/modules/t/dnaAlignFeatureAdaptor.t b/modules/t/dnaAlignFeatureAdaptor.t
index bf085052f6..ba361c1abd 100644
--- a/modules/t/dnaAlignFeatureAdaptor.t
+++ b/modules/t/dnaAlignFeatureAdaptor.t
@@ -2,7 +2,7 @@ use strict;
BEGIN { $| = 1;
use Test;
- plan tests => 23;
+ plan tests => 25;
}
@@ -97,6 +97,8 @@ my $score = 80;
my $percent_id = 90;
my $evalue = 23.2;
my $cigar_string = '100M';
+my $hcoverage = 99.5;
+my $external_db_id = 2200;
$feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
(-START => $start,
@@ -111,7 +113,9 @@ $feat = Bio::EnsEMBL::DnaDnaAlignFeature->new
-PERCENT_ID => $percent_id,
-SCORE => $score,
-P_VALUE => $evalue,
- -ANALYSIS => $analysis);
+ -ANALYSIS => $analysis,
+ -HCOVERAGE => $hcoverage,
+ -EXTERNAL_DB_ID => $external_db_id );
ok(!$feat->is_stored($db));
@@ -137,6 +141,8 @@ ok($feat->percent_id == $percent_id);
ok($feat->score == $score);
ok($feat->p_value == $evalue);
ok($feat->analysis->logic_name eq $analysis->logic_name);
+ok($feat->external_db_id == $external_db_id);
+ok($feat->hcoverage == $hcoverage);
$multi->restore('core', 'dna_align_feature');
diff --git a/modules/t/proteinAlignFeatureAdaptor.t b/modules/t/proteinAlignFeatureAdaptor.t
index 40a7ef23c2..a77796c5d3 100644
--- a/modules/t/proteinAlignFeatureAdaptor.t
+++ b/modules/t/proteinAlignFeatureAdaptor.t
@@ -1,7 +1,7 @@
BEGIN { $| = 1;
use Test;
- plan tests => 22;
+ plan tests => 24;
}
@@ -98,6 +98,8 @@ my $score = 80;
my $percent_id = 90;
my $evalue = 23.2;
my $cigar_string = '100M';
+my $hcoverage = 99.5;
+my $external_db_id = 2200;
$feat = Bio::EnsEMBL::DnaPepAlignFeature->new
(-START => $start,
@@ -112,7 +114,9 @@ $feat = Bio::EnsEMBL::DnaPepAlignFeature->new
-PERCENT_ID => $percent_id,
-SCORE => $score,
-P_VALUE => $evalue,
- -ANALYSIS => $analysis);
+ -ANALYSIS => $analysis,
+ -HCOVERAGE => $hcoverage,
+ -EXTERNAL_DB_ID => $external_db_id );
ok(!$feat->is_stored($db));
@@ -137,6 +141,8 @@ ok($feat->percent_id == $percent_id);
ok($feat->score == $score);
ok($feat->p_value == $evalue);
ok($feat->analysis->logic_name eq $analysis->logic_name);
+ok($feat->external_db_id == $external_db_id);
+ok($feat->hcoverage == $hcoverage);
$multi->restore('core', 'protein_align_feature');
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.sql b/modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.sql
index f9a0c7ef39..6826653e95 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/dna_align_feature.sql
@@ -13,10 +13,13 @@ CREATE TABLE `dna_align_feature` (
`evalue` double default NULL,
`perc_ident` float default NULL,
`cigar_line` text collate latin1_bin,
- PRIMARY KEY (`dna_align_feature_id`),
+ `external_db_id` smallint(5) unsigned default NULL,
+ `hcoverage` double default NULL,
+ PRIMARY KEY (`dna_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
- KEY `analysis_idx` (`analysis_id`)
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `external_db_idx` (`external_db_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 54d2f95a04..f0e5d39ec1 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -1,4 +1,4 @@
-1 schema_version 46
+1 schema_version 47
2 assembly.default NCBI34
33 species.classification Chordata
32 species.classification Vertebrata
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.sql b/modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.sql
index c9bd049aab..b6802ca534 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/protein_align_feature.sql
@@ -11,11 +11,14 @@ CREATE TABLE `protein_align_feature` (
`score` double default NULL,
`evalue` double default NULL,
`perc_ident` float default NULL,
- `cigar_line` text collate latin1_bin,
- PRIMARY KEY (`protein_align_feature_id`),
+ `cigar_line` text collate latin1_bin,
+ `external_db_id` smallint(5) unsigned default NULL,
+ `hcoverage` double default NULL,
+ PRIMARY KEY (`protein_align_feature_id`),
KEY `seq_region_idx` (`seq_region_id`,`analysis_id`,`seq_region_start`,`score`),
KEY `seq_region_idx_2` (`seq_region_id`,`seq_region_start`),
KEY `hit_idx` (`hit_name`),
- KEY `analysis_idx` (`analysis_id`)
+ KEY `analysis_idx` (`analysis_id`),
+ KEY `external_db_idx` (`external_db_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
--
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